data_19175 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; [Asp2]RTD-1 ; _BMRB_accession_number 19175 _BMRB_flat_file_name bmr19175.str _Entry_type original _Submission_date 2013-04-18 _Accession_date 2013-04-18 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details 'High resolution NMR solution structure of a theta-defensin analogue containing the RGD integrin-binding sequence. Head-to-tail (Arg-Gly) cyclic peptide.' loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conibear Anne C. . 2 Bochen Alexander . . 3 Rosengren 'K. Johan' . . 4 Kessler Horst . . 5 Craik David J. . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 102 "13C chemical shifts" 52 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-02-05 update author 'update entry citation' 2014-02-03 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 18723 'High resolution NMR solution structure of the theta-defensin RTD-1' 19176 [Asp11]RTD-1 19177 [Asp2,11]RTD-1 stop_ save_ ############################# # Citation for this entry # ############################# save_RGD_peptides _Saveframe_category entry_citation _Citation_full . _Citation_title 'The Cyclic Cystine Ladder of Theta-Defensins as a Stable, Bifunctional Scaffold: A Proof-of-Concept Study Using the Integrin-Binding RGD Motif' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 24382674 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Conibear Anne C. . 2 Bochen Alexander . . 3 Rosengren 'K. Johan' . . 4 Stupar Petar . . 5 Wang Conan . . 6 Kessler Horst . . 7 Craik David J. . stop_ _Journal_abbreviation ChemBioChem _Journal_volume 15 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 451 _Page_last 459 _Year 2014 _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name [Asp2]RTD-1 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label [Asp2]RTD-1 $entity stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common [Asp2]RTD-1 _Molecular_mass 2078.569 _Mol_thiol_state 'all disulfide bound' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 18 _Mol_residue_sequence GDCRCLCRRGVCRCICTR loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 GLY 2 2 ASP 3 3 CYS 4 4 ARG 5 5 CYS 6 6 LEU 7 7 CYS 8 8 ARG 9 9 ARG 10 10 GLY 11 11 VAL 12 12 CYS 13 13 ARG 14 14 CYS 15 15 ILE 16 16 CYS 17 17 THR 18 18 ARG stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-11-04 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value PDB 2M77 [asp2]rtd-1 100.00 18 100.00 100.00 3.31e-01 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $entity 'Rhesus monkey' 9544 Eukaryota Metazoa Macaca mulatta stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name _Details $entity 'chemical synthesis' . . . . . 'Solid phase peptide synthesis' stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details '0.7 mM, pH 3' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 0.7 mM 'natural abundance' DSS 10 ug 'natural abundance' H2O 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details '0.6 mM, pH 3' loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity 0.6 mM 'natural abundance' DSS 10 ug 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_CcpNmr _Saveframe_category software _Name CcpNMR _Version 2.1 loop_ _Vendor _Address _Electronic_address CCPN . http://www.ccpn.ac.uk/software/analysis stop_ loop_ _Task 'chemical shift assignment' 'data analysis' 'peak picking' stop_ _Details . save_ save_TOPSPIN _Saveframe_category software _Name TOPSPIN _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Bruker Biospin' . . stop_ loop_ _Task collection processing stop_ _Details . save_ save_CYANA _Saveframe_category software _Name CYANA _Version 3.0 loop_ _Vendor _Address _Electronic_address 'Guntert, Mumenthaler and Wuthrich' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ save_CNS _Saveframe_category software _Name CNS _Version 2.1 loop_ _Vendor _Address _Electronic_address 'Brunger, Adams, Clore, Gros, Nilges and Read' . . stop_ loop_ _Task refinement stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_2D_1H-1H_TOCSY_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC' _Sample_label $sample_2 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_ECOSY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H ECOSY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 3 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS C 13 'methyl protons' ppm 0.00 internal indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D 1H-13C HSQC' stop_ loop_ _Sample_label $sample_1 $sample_2 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name [Asp2]RTD-1 _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 GLY HA2 H 3.663 0.006 2 2 1 1 GLY HA3 H 4.134 0.005 2 3 1 1 GLY H H 8.601 0.003 1 4 1 1 GLY CA C 45.375 0.009 1 5 2 2 ASP H H 7.917 0.003 1 6 2 2 ASP HA H 5.006 0.011 1 7 2 2 ASP HB2 H 2.998 0.005 2 8 2 2 ASP HB3 H 2.758 0.002 2 9 2 2 ASP CA C 51.831 0.050 1 10 2 2 ASP CB C 39.095 0.013 1 11 3 3 CYS H H 8.877 0.003 1 12 3 3 CYS HA H 5.420 0.007 1 13 3 3 CYS HB2 H 2.636 0.003 2 14 3 3 CYS HB3 H 3.012 0.007 2 15 3 3 CYS CA C 55.810 0.050 1 16 3 3 CYS CB C 47.083 0.023 1 17 4 4 ARG H H 8.714 0.001 1 18 4 4 ARG HA H 4.698 0.008 1 19 4 4 ARG HB2 H 1.830 0.005 2 20 4 4 ARG HB3 H 1.830 0.005 2 21 4 4 ARG HG2 H 1.654 0.050 2 22 4 4 ARG HG3 H 1.654 0.050 2 23 4 4 ARG HD2 H 3.226 0.007 2 24 4 4 ARG HD3 H 3.226 0.007 2 25 4 4 ARG HE H 7.278 0.050 1 26 4 4 ARG CA C 55.074 0.050 1 27 4 4 ARG CB C 32.564 0.050 1 28 4 4 ARG CD C 43.291 0.050 1 29 5 5 CYS H H 9.066 0.005 1 30 5 5 CYS HA H 5.549 0.002 1 31 5 5 CYS HB2 H 3.038 0.008 2 32 5 5 CYS HB3 H 2.626 0.005 2 33 5 5 CYS CA C 55.553 0.050 1 34 5 5 CYS CB C 48.244 0.048 1 35 6 6 LEU H H 8.697 0.002 1 36 6 6 LEU HA H 4.720 0.001 1 37 6 6 LEU HB2 H 1.665 0.005 2 38 6 6 LEU HB3 H 1.665 0.005 2 39 6 6 LEU HG H 1.568 0.003 1 40 6 6 LEU HD1 H 0.925 0.002 2 41 6 6 LEU HD2 H 0.925 0.002 2 42 6 6 LEU CA C 54.488 0.050 1 43 6 6 LEU CB C 44.523 0.050 1 44 6 6 LEU CG C 27.382 0.050 1 45 6 6 LEU CD1 C 24.578 0.050 1 46 6 6 LEU CD2 C 24.578 0.050 1 47 7 7 CYS H H 9.116 0.016 1 48 7 7 CYS HA H 5.544 0.009 1 49 7 7 CYS HB2 H 3.080 0.026 2 50 7 7 CYS HB3 H 2.665 0.035 2 51 7 7 CYS CA C 55.427 0.050 1 52 7 7 CYS CB C 48.082 0.018 1 53 8 8 ARG H H 8.689 0.001 1 54 8 8 ARG HA H 4.535 0.003 1 55 8 8 ARG HB2 H 1.794 0.005 2 56 8 8 ARG HB3 H 1.794 0.005 2 57 8 8 ARG HG2 H 1.565 0.038 2 58 8 8 ARG HG3 H 1.565 0.038 2 59 8 8 ARG HD2 H 3.226 0.050 2 60 8 8 ARG HD3 H 3.226 0.050 2 61 8 8 ARG HE H 7.250 0.050 1 62 8 8 ARG CA C 55.650 0.050 1 63 8 8 ARG CB C 32.914 0.050 1 64 8 8 ARG CG C 27.054 0.050 1 65 8 8 ARG CD C 43.459 0.050 1 66 9 9 ARG H H 9.555 0.002 1 67 9 9 ARG HA H 3.930 0.003 1 68 9 9 ARG HB2 H 2.078 0.005 2 69 9 9 ARG HB3 H 1.838 0.002 2 70 9 9 ARG HG2 H 1.633 0.005 2 71 9 9 ARG HG3 H 1.633 0.005 2 72 9 9 ARG HD2 H 3.243 0.007 2 73 9 9 ARG HD3 H 3.243 0.007 2 74 9 9 ARG HE H 7.237 0.050 1 75 9 9 ARG CA C 57.038 0.050 1 76 9 9 ARG CB C 28.140 0.022 1 77 9 9 ARG CG C 27.953 0.050 1 78 9 9 ARG CD C 43.321 0.050 1 79 10 10 GLY H H 8.683 0.003 1 80 10 10 GLY HA2 H 3.605 0.002 2 81 10 10 GLY HA3 H 4.168 0.003 2 82 10 10 GLY CA C 45.384 0.017 1 83 11 11 VAL H H 7.804 0.004 1 84 11 11 VAL HA H 4.321 0.003 1 85 11 11 VAL HB H 2.131 0.007 1 86 11 11 VAL HG1 H 0.941 0.007 2 87 11 11 VAL HG2 H 0.941 0.007 2 88 11 11 VAL CA C 61.733 0.050 1 89 11 11 VAL CB C 33.527 0.050 1 90 11 11 VAL CG1 C 20.683 0.050 1 91 11 11 VAL CG2 C 21.058 0.050 1 92 12 12 CYS H H 9.040 0.050 1 93 12 12 CYS HA H 5.513 0.014 1 94 12 12 CYS HB2 H 3.046 0.017 2 95 12 12 CYS HB3 H 2.626 0.003 2 96 12 12 CYS CA C 55.335 0.050 1 97 12 12 CYS CB C 48.010 0.042 1 98 13 13 ARG H H 8.673 0.001 1 99 13 13 ARG HA H 4.704 0.001 1 100 13 13 ARG HB2 H 1.854 0.008 2 101 13 13 ARG HB3 H 1.854 0.008 2 102 13 13 ARG HG2 H 1.586 0.003 2 103 13 13 ARG HG3 H 1.664 0.005 2 104 13 13 ARG HD2 H 3.220 0.005 2 105 13 13 ARG HD3 H 3.220 0.005 2 106 13 13 ARG HE H 7.215 0.050 1 107 13 13 ARG CA C 55.056 0.050 1 108 13 13 ARG CB C 32.441 0.050 1 109 13 13 ARG CG C 27.322 0.006 1 110 13 13 ARG CD C 43.327 0.050 1 111 14 14 CYS H H 9.104 0.001 1 112 14 14 CYS HA H 5.568 0.006 1 113 14 14 CYS HB2 H 3.083 0.008 2 114 14 14 CYS HB3 H 2.645 0.008 2 115 14 14 CYS CA C 55.443 0.050 1 116 14 14 CYS CB C 48.220 0.048 1 117 15 15 ILE H H 8.794 0.001 1 118 15 15 ILE HA H 4.415 0.005 1 119 15 15 ILE HB H 1.838 0.002 1 120 15 15 ILE HG12 H 1.150 0.004 2 121 15 15 ILE HG13 H 1.524 0.002 2 122 15 15 ILE HG2 H 0.911 0.005 1 123 15 15 ILE HD1 H 0.894 0.008 1 124 15 15 ILE CA C 60.372 0.050 1 125 15 15 ILE CB C 40.434 0.050 1 126 15 15 ILE CG1 C 27.434 0.021 1 127 15 15 ILE CG2 C 17.272 0.050 1 128 15 15 ILE CD1 C 13.025 0.050 1 129 16 16 CYS H H 9.127 0.015 1 130 16 16 CYS HA H 5.538 0.007 1 131 16 16 CYS HB2 H 3.097 0.015 2 132 16 16 CYS HB3 H 2.709 0.028 2 133 16 16 CYS CA C 55.530 0.050 1 134 16 16 CYS CB C 47.986 0.006 1 135 17 17 THR H H 8.616 0.004 1 136 17 17 THR HA H 4.454 0.006 1 137 17 17 THR HB H 4.131 0.007 1 138 17 17 THR HG2 H 1.222 0.001 1 139 17 17 THR CA C 61.140 0.050 1 140 17 17 THR CB C 70.290 0.050 1 141 17 17 THR CG2 C 21.210 0.050 1 142 18 18 ARG H H 9.433 0.002 1 143 18 18 ARG HA H 3.913 0.002 1 144 18 18 ARG HB2 H 2.018 0.005 2 145 18 18 ARG HB3 H 1.885 0.004 2 146 18 18 ARG HG2 H 1.660 0.010 2 147 18 18 ARG HG3 H 1.660 0.010 2 148 18 18 ARG HD2 H 3.260 0.006 2 149 18 18 ARG HD3 H 3.260 0.006 2 150 18 18 ARG HE H 7.255 0.050 1 151 18 18 ARG CA C 57.278 0.050 1 152 18 18 ARG CB C 28.329 0.011 1 153 18 18 ARG CG C 27.930 0.050 1 154 18 18 ARG CD C 43.465 0.050 1 stop_ save_